10 20 30 40 50 60 70 80 2P2Y - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER HYDROLASE 08-MAR-07 2P2Y
TITLE CRYSTAL STRUCTURE OF TTHB049 FROM THERMUS THERMOPHILUS HB8
COMPND MOL_ID: 1; COMPND 2 MOLECULE: ALPHA-RIBAZOLE-5'-PHOSPHATE PHOSPHATASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: TTHB049 PROTEIN; COMPND 5 EC: 3.1.3.73; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES
SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: THERMUS THERMOPHILUS; SOURCE 3 ORGANISM_TAXID: 274; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 5 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PET-11A
KEYWDS HYDROLASE, STRUCTURAL GENOMICS, NPPSFA, NATIONAL PROJECT ON KEYWDS 2 PROTEIN STRUCTURAL AND FUNCTIONAL ANALYSES, RIKEN KEYWDS 3 STRUCTURAL GENOMICS/PROTEOMICS INITIATIVE, RSGI
EXPDTA X-RAY DIFFRACTION
AUTHOR M.SUGAHARA,Y.MORIKAWA,M.TAKETA,Y.MATSUURA,N.KUNISHIMA,RIKEN AUTHOR 2 STRUCTURAL GENOMICS/PROTEOMICS INITIATIVE (RSGI)
REVDAT 2 24-FEB-09 2P2Y 1 VERSN REVDAT 1 11-SEP-07 2P2Y 0
JRNL AUTH M.SUGAHARA,Y.MORIKAWA,M.TAKETA,Y.MATSUURA, JRNL AUTH 2 N.KUNISHIMA JRNL TITL CRYSTAL STRUCTURE OF TTHB049 FROM THERMUS JRNL TITL 2 THERMOPHILUS HB8 JRNL REF TO BE PUBLISHED JRNL REFN
REMARK 1
REMARK 2 REMARK 2 RESOLUTION. 1.95 ANGSTROMS.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.1 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES, PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.95 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.83 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 11227 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.225 REMARK 3 FREE R VALUE : 0.254 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 546 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1343 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 1 REMARK 3 SOLVENT ATOMS : 158 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 23.90 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 28.30 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 2.27000 REMARK 3 B22 (A**2) : 2.27000 REMARK 3 B33 (A**2) : -4.54000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.26 REMARK 3 ESD FROM SIGMAA (A) : 0.22 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.31 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.24 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 1.400 REMARK 3 BOND ANGLES (DEGREES) : 0.01 REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : ANISOTROP REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : NULL REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4 REMARK 4 2P2Y COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 13-APR-07. REMARK 100 THE RCSB ID CODE IS RCSB041899.
REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 27-DEC-06 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.8 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 11290 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.950 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 11.000 REMARK 200 R MERGE (I) : 0.04100 REMARK 200 R SYM (I) : 0.04000 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 15.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.95 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.02 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.0 REMARK 200 DATA REDUNDANCY IN SHELL : 10.20 REMARK 200 R MERGE FOR SHELL (I) : 0.11900 REMARK 200 R SYM FOR SHELL (I) : 0.11500 REMARK 200 <I/SIGMA(I)> FOR SHELL : 9.700 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: FOURIER SYNTHESIS REMARK 200 SOFTWARE USED: CNS REMARK 200 STARTING MODEL: 1V7Q REMARK 200 REMARK 200 REMARK: NULL
REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 32.01 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.81 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 2.75M NACL, 0.1M CITRATE, PH 4.8, REMARK 280 OIL MICRO BATCH, TEMPERATURE 295K
REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+3/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+3/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 78.42400 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 21.29600 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 21.29600 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 39.21200 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 21.29600 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 21.29600 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 117.63600 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 21.29600 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 21.29600 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 39.21200 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 21.29600 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 21.29600 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 117.63600 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 78.42400 REMARK 290 REMARK 290 REMARK: NULL
REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 300 REMARK: THE BIOLOGICAL ASSEMBLY IS A MONOMER IN THE ASYMMETRIC REMARK 300 UNIT.
REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000
REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 ASP A 171 REMARK 465 GLY A 172 REMARK 465 GLU A 173 REMARK 465 GLU A 174 REMARK 465 ALA A 175 REMARK 465 THR A 176 REMARK 465 GLY A 177
REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 THR A 132 -151.62 -133.89 REMARK 500 PRO A 161 43.97 -101.72 REMARK 500 ARG A 162 -65.80 -104.19 REMARK 500 REMARK 500 REMARK: NULL
REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A1102 DISTANCE = 5.09 ANGSTROMS
REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 1001
REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2P30 RELATED DB: PDB REMARK 900 RELATED ID: TTK003000215.8 RELATED DB: TARGETDB
DBREF 2P2Y A 1 177 UNP Q53WB3 Q53WB3_THET8 1 177
SEQADV 2P2Y MET A 5 UNP Q53WB3 LEU 5 ENGINEERED
SEQRES 1 A 177 MET GLU LEU TRP MET VAL ARG HIS GLY GLU THR LEU TRP SEQRES 2 A 177 ASN ARG GLU GLY ARG LEU LEU GLY TRP THR ASP LEU PRO SEQRES 3 A 177 LEU THR ALA GLU GLY GLU ALA GLN ALA ARG ARG LEU LYS SEQRES 4 A 177 GLY ALA LEU PRO SER LEU PRO ALA PHE SER SER ASP LEU SEQRES 5 A 177 LEU ARG ALA ARG ARG THR ALA GLU LEU ALA GLY PHE SER SEQRES 6 A 177 PRO ARG LEU TYR PRO GLU LEU ARG GLU ILE HIS PHE GLY SEQRES 7 A 177 ALA LEU GLU GLY ALA LEU TRP GLU THR LEU ASP PRO ARG SEQRES 8 A 177 TYR LYS GLU ALA LEU LEU ARG PHE GLN GLY PHE HIS PRO SEQRES 9 A 177 PRO GLY GLY GLU SER LEU SER ALA PHE GLN GLU ARG VAL SEQRES 10 A 177 PHE ARG PHE LEU GLU GLY LEU LYS ALA PRO ALA VAL LEU SEQRES 11 A 177 PHE THR HIS GLY GLY VAL VAL ARG ALA VAL LEU ARG ALA SEQRES 12 A 177 LEU GLY GLU ASP GLY LEU VAL PRO PRO GLY SER ALA VAL SEQRES 13 A 177 ALA VAL ASP TRP PRO ARG ARG VAL LEU VAL ARG LEU ALA SEQRES 14 A 177 LEU ASP GLY GLU GLU ALA THR GLY
HET CL A1001 1
HETNAM CL CHLORIDE ION
FORMUL 2 CL CL 1- FORMUL 3 HOH *158(H2 O)
HELIX 1 1 THR A 11 GLY A 17 1 7 HELIX 2 2 THR A 28 LYS A 39 1 12 HELIX 3 3 LEU A 52 ALA A 62 1 11 HELIX 4 4 PRO A 70 ARG A 73 5 4 HELIX 5 5 PHE A 77 GLU A 81 5 5 HELIX 6 6 ASP A 89 PHE A 99 1 11 HELIX 7 7 SER A 109 GLY A 123 1 15 HELIX 8 8 HIS A 133 LEU A 144 1 12
SHEET 1 A 6 ARG A 67 LEU A 68 0 SHEET 2 A 6 ALA A 47 SER A 49 1 N SER A 49 O ARG A 67 SHEET 3 A 6 ALA A 128 THR A 132 1 O PHE A 131 N PHE A 48 SHEET 4 A 6 GLU A 2 ARG A 7 1 N TRP A 4 O LEU A 130 SHEET 5 A 6 ALA A 155 ASP A 159 -1 O VAL A 156 N MET A 5 SHEET 6 A 6 ARG A 163 LEU A 168 -1 O VAL A 166 N ALA A 157
CISPEP 1 TRP A 160 PRO A 161 0 -0.04
SITE 1 AC1 5 ARG A 7 HIS A 8 ASN A 14 GLY A 134 SITE 2 AC1 5 HOH A1006
CRYST1 42.592 42.592 156.848 90.00 90.00 90.00 P 41 21 2 8
ORIGX1 1.000000 0.000000 0.000000 0.00000
ORIGX2 0.000000 1.000000 0.000000 0.00000
ORIGX3 0.000000 0.000000 1.000000 0.00000
SCALE1 0.023479 0.000000 0.000000 0.00000
SCALE2 0.000000 0.023479 0.000000 0.00000
SCALE3 0.000000 0.000000 0.006376 0.00000